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Abstract:

Evolutionary forces may act on the genome at different levels, from the change of single nucleotides to the duplication or rearrangement of whole chromosomes. Some of these evolutionary processes can be responsible for changes at different levels, while others will be more specifc. In this work we will examine changes in the genome at two different levels, at the genomic level by identifying changes in gene order and content, and at the gene level by identifying cases of intron gain and loss. Identification of these changes as well as the mechanisms that are responsible for them will allow a better understanding of the processes involved in the evolution of the genome. In the first part of this work we used the genome sequence available for the three primates Homo sapiens, Pan troglodytes and Macaca mulatta in order to build a set of synteny blocks where gene order is conserved. This was done for each pair of species and the resulting blocks confirmed the high level of similarity between the three genomes, with most of their genes included within the blocks. We classifed all protein-coding genes within the synteny blocks and identified those that are conserved between each pair of species as well as those that are present on the three species as one-to-one orthologues, which included more than half of the human genes. We also identifed gene duplications and translocation within the identifed synteny blocks. Where differences in gene content were found we examined the assembly information and genome annotation in order to determine which of these differences were reliable and which ones may be due to assembly or annotation errors. In the case of human and chimpanzee, those cases that were identifed as reliable differences between the two species were compared to the macaque in order to identify lineage speci.c di.erences that had occurred since the chimpanzee and human lineages diverged. These lineage specific genes were further exam­ined and we identifed nine cases in which an origin by exaptation of non-coding DNA could not be ruled out. We also searched for cases of alternatively spliced genes that may have become duplicated and undergone subsequent subfunctionalization, by differential loss of splice variants, since the divergence of the human and chimpanzee lineage. We identifed one alternatively spliced gene that was duplicated specifically in the human lineage where the two copies show different alternative splice forms annotated. However, we could not find unambiguous evidence at the sequence level of the inability of either copy to produce all of these variants. In the second part of this study we identified those introns that had been differentially gained or lost between pairs of paralogous genes that originated simultaneously in a large genome duplication that occurred in Arabidopsis thaliana 20 -60 Mya. We found a high rate of intron turnover since the duplication event, although with the available data we were only able to identify a small fraction of the inserted/deleted introns unambiguously as gains our losses. Despite the relatively recent origin of the new introns we identifed, only in one case were we able to identify the precise mechanism by which a new intron had originated.